Program: gdcm
Module: $RCSfile: gdcmDocument.cxx,v $
Language: C++
- Date: $Date: 2004/09/22 21:01:55 $
- Version: $Revision: 1.87 $
+ Date: $Date: 2004/10/20 14:30:40 $
+ Version: $Revision: 1.106 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
- http://www.creatis.insa-lyon.fr/Public/Gdcm/License.htm for details.
+ http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
This software is distributed WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
#include "gdcmValEntry.h"
#include "gdcmBinEntry.h"
#include "gdcmSeqEntry.h"
-
#include "gdcmGlobal.h"
#include "gdcmUtil.h"
#include "gdcmDebug.h"
#include <netinet/in.h>
#endif
-# include <iomanip>
+#include <iomanip>
+
+namespace gdcm
+{
// Implicit VR Little Endian
#define UI1_2_840_10008_1_2 "1.2.840.10008.1.2"
#define str2num(str, typeNum) *((typeNum *)(str))
//-----------------------------------------------------------------------------
-// Refer to gdcmDocument::CheckSwap()
-const unsigned int gdcmDocument::HEADER_LENGTH_TO_READ = 256;
+// Refer to Document::CheckSwap()
+const unsigned int Document::HEADER_LENGTH_TO_READ = 256;
-// Refer to gdcmDocument::SetMaxSizeLoadEntry()
-const unsigned int gdcmDocument::MAX_SIZE_LOAD_ELEMENT_VALUE = 0xfff; // 4096
-const unsigned int gdcmDocument::MAX_SIZE_PRINT_ELEMENT_VALUE = 0x7fffffff;
+// Refer to Document::SetMaxSizeLoadEntry()
+const unsigned int Document::MAX_SIZE_LOAD_ELEMENT_VALUE = 0xfff; // 4096
+const unsigned int Document::MAX_SIZE_PRINT_ELEMENT_VALUE = 0x7fffffff;
//-----------------------------------------------------------------------------
// Constructor / Destructor
* \brief constructor
* @param filename file to be opened for parsing
*/
-gdcmDocument::gdcmDocument( std::string const & filename )
- : gdcmElementSet(-1)
+Document::Document( std::string const & filename )
+ : ElementSet(-1)
{
SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE);
Filename = filename;
return;
}
- dbg.Verbose(0, "gdcmDocument::gdcmDocument: starting parsing of file: ",
+ dbg.Verbose(0, "Document::Document: starting parsing of file: ",
Filename.c_str());
rewind(Fp);
long beg = ftell(Fp);
lgt -= beg;
- (void)ParseDES( this, beg, lgt, false); // le Load sera fait a la volee
+ ParseDES( this, beg, lgt, false); // le Load sera fait a la volee
rewind(Fp);
std::string PhotometricInterpretation = GetEntryByNumber(0x0028,0x0004);
if( PhotometricInterpretation == "PALETTE COLOR " )
{
- LoadEntryVoidArea(0x0028,0x1200); // gray LUT
+ LoadEntryBinArea(0x0028,0x1200); // gray LUT
/// FIXME FIXME FIXME
/// The tags refered by the three following lines used to be CORRECTLY
/// defined as having an US Value Representation in the public
/// dictionnary. BUT the semantics implied by the three following
/// lines state that the corresponding tag contents are in fact
- /// the ones of a gdcmBinEntry.
+ /// the ones of a BinEntry.
/// In order to fix things "Quick and Dirty" the dictionnary was
/// altered on PURPOUS but now contains a WRONG value.
/// In order to fix things and restore the dictionary to its
/// correct value, one needs to decided of the semantics by deciding
/// wether the following tags are either:
- /// - multivaluated US, and hence loaded as gdcmValEntry, but afterwards
- /// also used as gdcmBinEntry, which requires the proper conversion,
- /// - OW, and hence loaded as gdcmBinEntry, but afterwards also used
- /// as gdcmValEntry, which requires the proper conversion.
- LoadEntryVoidArea(0x0028,0x1201); // R LUT
- LoadEntryVoidArea(0x0028,0x1202); // G LUT
- LoadEntryVoidArea(0x0028,0x1203); // B LUT
+ /// - multivaluated US, and hence loaded as ValEntry, but afterwards
+ /// also used as BinEntry, which requires the proper conversion,
+ /// - OW, and hence loaded as BinEntry, but afterwards also used
+ /// as ValEntry, which requires the proper conversion.
+ LoadEntryBinArea(0x0028,0x1201); // R LUT
+ LoadEntryBinArea(0x0028,0x1202); // G LUT
+ LoadEntryBinArea(0x0028,0x1203); // B LUT
// Segmented Red Palette Color LUT Data
- LoadEntryVoidArea(0x0028,0x1221);
+ LoadEntryBinArea(0x0028,0x1221);
// Segmented Green Palette Color LUT Data
- LoadEntryVoidArea(0x0028,0x1222);
+ LoadEntryBinArea(0x0028,0x1222);
// Segmented Blue Palette Color LUT Data
- LoadEntryVoidArea(0x0028,0x1223);
+ LoadEntryBinArea(0x0028,0x1223);
}
//FIXME later : how to use it?
- LoadEntryVoidArea(0x0028,0x3006); //LUT Data (CTX dependent)
+ LoadEntryBinArea(0x0028,0x3006); //LUT Data (CTX dependent)
CloseFile();
RecCode == "CANRME_AILIBOD1_1." ) // for brain-damaged softwares
// with "little-endian strings"
{
- Filetype = gdcmACR_LIBIDO;
+ Filetype = ACR_LIBIDO;
std::string rows = GetEntryByNumber(0x0028, 0x0010);
std::string columns = GetEntryByNumber(0x0028, 0x0011);
SetEntryByNumber(columns, 0x0028, 0x0010);
/**
* \brief This default constructor doesn't parse the file. You should
- * then invoke \ref gdcmDocument::SetFileName and then the parsing.
+ * then invoke \ref Document::SetFileName and then the parsing.
*/
-gdcmDocument::gdcmDocument()
- :gdcmElementSet(-1)
+Document::Document()
+ :ElementSet(-1)
{
SetMaxSizeLoadEntry(MAX_SIZE_LOAD_ELEMENT_VALUE);
Initialise();
/**
* \brief Canonical destructor.
*/
-gdcmDocument::~gdcmDocument ()
+Document::~Document ()
{
- RefPubDict = 0;
- RefShaDict = 0;
+ RefPubDict = NULL;
+ RefShaDict = NULL;
+
+ // Recursive clean up of sequences
+ for (TagDocEntryHT::const_iterator it = TagHT.begin();
+ it != TagHT.end(); ++it )
+ {
+ //delete it->second; //temp remove
+ }
+ TagHT.clear();
}
//-----------------------------------------------------------------------------
* \brief Prints The Dict Entries of THE public Dicom Dictionary
* @return
*/
-void gdcmDocument::PrintPubDict(std::ostream & os)
+void Document::PrintPubDict(std::ostream & os)
{
RefPubDict->Print(os);
}
* \brief Prints The Dict Entries of THE shadow Dicom Dictionary
* @return
*/
-void gdcmDocument::PrintShaDict(std::ostream & os)
+void Document::PrintShaDict(std::ostream & os)
{
RefShaDict->Print(os);
}
/**
* \brief Get the public dictionary used
*/
-gdcmDict *gdcmDocument::GetPubDict()
+Dict* Document::GetPubDict()
{
return RefPubDict;
}
/**
* \brief Get the shadow dictionary used
*/
-gdcmDict *gdcmDocument::GetShaDict()
+Dict* Document::GetShaDict()
{
return RefShaDict;
}
* \brief Set the shadow dictionary used
* \param dict dictionary to use in shadow
*/
-bool gdcmDocument::SetShaDict(gdcmDict *dict)
+bool Document::SetShaDict(Dict *dict)
{
RefShaDict = dict;
return !RefShaDict;
* \brief Set the shadow dictionary used
* \param dictName name of the dictionary to use in shadow
*/
-bool gdcmDocument::SetShaDict(DictKey const & dictName)
+bool Document::SetShaDict(DictKey const & dictName)
{
- RefShaDict = gdcmGlobal::GetDicts()->GetDict(dictName);
+ RefShaDict = Global::GetDicts()->GetDict(dictName);
return !RefShaDict;
}
/**
* \brief This predicate, based on hopefully reasonable heuristics,
- * decides whether or not the current gdcmDocument was properly parsed
+ * decides whether or not the current Document was properly parsed
* and contains the mandatory information for being considered as
* a well formed and usable Dicom/Acr File.
- * @return true when gdcmDocument is the one of a reasonable Dicom/Acr file,
+ * @return true when Document is the one of a reasonable Dicom/Acr file,
* false otherwise.
*/
-bool gdcmDocument::IsReadable()
+bool Document::IsReadable()
{
- if( Filetype == gdcmUnknown)
+ if( Filetype == Unknown)
{
- dbg.Verbose(0, "gdcmDocument::IsReadable: wrong filetype");
+ dbg.Verbose(0, "Document::IsReadable: wrong filetype");
return false;
}
if( TagHT.empty() )
{
- dbg.Verbose(0, "gdcmDocument::IsReadable: no tags in internal"
+ dbg.Verbose(0, "Document::IsReadable: no tags in internal"
" hash table.");
return false;
}
* the current document. False either when the document contains
* no Transfer Syntax, or when the Tranfer Syntaxes doesn't match.
*/
-bool gdcmDocument::IsGivenTransferSyntax(std::string const & syntaxToCheck)
+bool Document::IsGivenTransferSyntax(std::string const & syntaxToCheck)
{
- gdcmDocEntry *entry = GetDocEntryByNumber(0x0002, 0x0010);
+ DocEntry *entry = GetDocEntryByNumber(0x0002, 0x0010);
if ( !entry )
{
return false;
// The entry might be present but not loaded (parsing and loading
// happen at different stages): try loading and proceed with check...
LoadDocEntrySafe(entry);
- if (gdcmValEntry* valEntry = dynamic_cast< gdcmValEntry* >(entry) )
+ if (ValEntry* valEntry = dynamic_cast< ValEntry* >(entry) )
{
std::string transfer = valEntry->GetValue();
// The actual transfer (as read from disk) might be padded. We
* \brief Determines if the Transfer Syntax of the present document
* corresponds to a Implicit Value Representation of
* Little Endian.
- * \sa \ref gdcmDocument::IsGivenTransferSyntax.
+ * \sa \ref Document::IsGivenTransferSyntax.
* @return True when ImplicitVRLittleEndian found. False in all other cases.
*/
-bool gdcmDocument::IsImplicitVRLittleEndianTransferSyntax()
+bool Document::IsImplicitVRLittleEndianTransferSyntax()
{
return IsGivenTransferSyntax(UI1_2_840_10008_1_2);
}
* and if it corresponds to a ExplicitVRLittleEndian one.
* @return True when ExplicitVRLittleEndian found. False in all other cases.
*/
-bool gdcmDocument::IsExplicitVRLittleEndianTransferSyntax()
+bool Document::IsExplicitVRLittleEndianTransferSyntax()
{
return IsGivenTransferSyntax(UI1_2_840_10008_1_2_1);
}
* and if it corresponds to a DeflatedExplicitVRLittleEndian one.
* @return True when DeflatedExplicitVRLittleEndian found. False in all other cases.
*/
-bool gdcmDocument::IsDeflatedExplicitVRLittleEndianTransferSyntax()
+bool Document::IsDeflatedExplicitVRLittleEndianTransferSyntax()
{
return IsGivenTransferSyntax(UI1_2_840_10008_1_2_1_99);
}
* and if it corresponds to a Explicit VR Big Endian one.
* @return True when big endian found. False in all other cases.
*/
-bool gdcmDocument::IsExplicitVRBigEndianTransferSyntax()
+bool Document::IsExplicitVRBigEndianTransferSyntax()
{
return IsGivenTransferSyntax(UI1_2_840_10008_1_2_2);
}
* and if it corresponds to a JPEGBaseLineProcess1 one.
* @return True when JPEGBaseLineProcess1found. False in all other cases.
*/
-bool gdcmDocument::IsJPEGBaseLineProcess1TransferSyntax()
+bool Document::IsJPEGBaseLineProcess1TransferSyntax()
{
return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_50);
}
* and if it corresponds to a JPEGExtendedProcess2-4 one.
* @return True when JPEGExtendedProcess2-4 found. False in all other cases.
*/
-bool gdcmDocument::IsJPEGExtendedProcess2_4TransferSyntax()
+bool Document::IsJPEGExtendedProcess2_4TransferSyntax()
{
return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_51);
}
* and if it corresponds to a JPEGExtendeProcess3-5 one.
* @return True when JPEGExtendedProcess3-5 found. False in all other cases.
*/
-bool gdcmDocument::IsJPEGExtendedProcess3_5TransferSyntax()
+bool Document::IsJPEGExtendedProcess3_5TransferSyntax()
{
return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_52);
}
* @return True when JPEGSpectralSelectionProcess6-8 found. False in all
* other cases.
*/
-bool gdcmDocument::IsJPEGSpectralSelectionProcess6_8TransferSyntax()
+bool Document::IsJPEGSpectralSelectionProcess6_8TransferSyntax()
{
return IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_53);
}
* @return True when RLE Lossless found. False in all
* other cases.
*/
-bool gdcmDocument::IsRLELossLessTransferSyntax()
+bool Document::IsRLELossLessTransferSyntax()
{
return IsGivenTransferSyntax(UI1_2_840_10008_1_2_5);
}
* other cases.
*/
-bool gdcmDocument::IsJPEGLossless()
+bool Document::IsJPEGLossless()
{
return ( IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_55)
|| IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_57)
* @return True when JPEG2000 (Lossly or LossLess) found. False in all
* other cases.
*/
-bool gdcmDocument::IsJPEG2000()
+bool Document::IsJPEG2000()
{
return ( IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_90)
|| IsGivenTransferSyntax(UI1_2_840_10008_1_2_4_91) );
}
+/**
+ * \brief Determines if the Transfer Syntax corresponds to any form
+ * of Jpeg encoded Pixel data.
+ * @return True when any form of JPEG found. False otherwise.
+ */
+bool Document::IsJPEGTransferSyntax()
+{
+ return ( IsJPEGBaseLineProcess1TransferSyntax()
+ || IsJPEGExtendedProcess2_4TransferSyntax()
+ || IsJPEGExtendedProcess3_5TransferSyntax()
+ || IsJPEGSpectralSelectionProcess6_8TransferSyntax()
+ || IsJPEGLossless()
+ || IsJPEG2000() );
+}
+
+
+/**
+ * \brief Determines if the Transfer Syntax corresponds to encapsulated
+ * of encoded Pixel Data (as opposed to native).
+ * @return True when encapsulated. False when native.
+ */
+bool Document::IsEncapsulateTransferSyntax()
+{
+ return ( IsJPEGTransferSyntax()
+ || IsRLELossLessTransferSyntax() );
+}
+
/**
* \brief Predicate for dicom version 3 file.
* @return True when the file is a dicom version 3.
*/
-bool gdcmDocument::IsDicomV3()
+bool Document::IsDicomV3()
{
// Checking if Transfert Syntax exists is enough
// Anyway, it's to late check if the 'Preamble' was found ...
* (ACR, ACR_LIBIDO, ExplicitVR, ImplicitVR, Unknown)
* @return the FileType code
*/
-FileType gdcmDocument::GetFileType()
+FileType Document::GetFileType()
{
return Filetype;
}
/**
- * \brief Tries to open the file \ref gdcmDocument::Filename and
+ * \brief Tries to open the file \ref Document::Filename and
* checks the preamble when existing.
* @return The FILE pointer on success.
*/
-FILE* gdcmDocument::OpenFile()
+FILE* Document::OpenFile()
{
Fp = fopen(Filename.c_str(),"rb");
if(!Fp)
{
dbg.Verbose( 0,
- "gdcmDocument::OpenFile cannot open file: ",
+ "Document::OpenFile cannot open file: ",
Filename.c_str());
return 0;
}
fclose(Fp);
dbg.Verbose( 0,
- "gdcmDocument::OpenFile not DICOM/ACR (missing preamble)",
+ "Document::OpenFile not DICOM/ACR (missing preamble)",
Filename.c_str());
return 0;
* \brief closes the file
* @return TRUE if the close was successfull
*/
-bool gdcmDocument::CloseFile()
+bool Document::CloseFile()
{
int closed = fclose(Fp);
Fp = 0;
* (ACR-NEMA, ExplicitVR, ImplicitVR)
* \return Always true.
*/
-void gdcmDocument::Write(FILE* fp,FileType filetype)
+void Document::Write(FILE* fp,FileType filetype)
{
/// \todo move the following lines (and a lot of others, to be written)
/// to a future function CheckAndCorrectHeader
/// (necessary if user wants to write a DICOM V3 file
- /// starting from an ACR-NEMA (V2) gdcmHeader
+ /// starting from an ACR-NEMA (V2) Header
- if (filetype == gdcmImplicitVR)
+ if (filetype == ImplicitVR)
{
std::string implicitVRTransfertSyntax = UI1_2_840_10008_1_2;
ReplaceOrCreateByNumber(implicitVRTransfertSyntax,0x0002, 0x0010);
SetEntryLengthByNumber(18, 0x0002, 0x0010);
}
- if (filetype == gdcmExplicitVR)
+ if (filetype == ExplicitVR)
{
std::string explicitVRTransfertSyntax = UI1_2_840_10008_1_2_1;
ReplaceOrCreateByNumber(explicitVRTransfertSyntax,0x0002, 0x0010);
* UpdateGroupLength(true,ACR);
*/
- gdcmElementSet::Write(fp, filetype); // This one is recursive
+ ElementSet::Write(fp, filetype); // This one is recursive
}
* \return pointer to the modified/created Header Entry (NULL when creation
* failed).
*/
-gdcmValEntry * gdcmDocument::ReplaceOrCreateByNumber(
+ValEntry* Document::ReplaceOrCreateByNumber(
std::string const & value,
uint16_t group,
uint16_t elem,
std::string const & VR )
{
- gdcmValEntry* valEntry = 0;
- gdcmDocEntry* currentEntry = GetDocEntryByNumber( group, elem);
+ ValEntry* valEntry = 0;
+ DocEntry* currentEntry = GetDocEntryByNumber( group, elem);
if (!currentEntry)
{
// check if (group,element) DictEntry exists
- // if it doesn't, create an entry in gdcmDictSet::VirtualEntry
+ // if it doesn't, create an entry in DictSet::VirtualEntry
// and use it
// Find out if the tag we received is in the dictionaries:
- gdcmDict *pubDict = gdcmGlobal::GetDicts()->GetDefaultPubDict();
- gdcmDictEntry *dictEntry = pubDict->GetDictEntryByNumber(group, elem);
+ Dict *pubDict = Global::GetDicts()->GetDefaultPubDict();
+ DictEntry* dictEntry = pubDict->GetDictEntryByNumber(group, elem);
if (!dictEntry)
{
currentEntry = NewDocEntryByNumber(group, elem,VR);
if (!currentEntry)
{
- dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: call to"
+ dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: call to"
" NewDocEntryByNumber failed.");
return NULL;
}
- valEntry = new gdcmValEntry(currentEntry);
+ valEntry = new ValEntry(currentEntry);
if ( !AddEntry(valEntry))
{
- dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: AddEntry"
+ dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: AddEntry"
" failed allthough this is a creation.");
}
}
else
{
- valEntry = dynamic_cast< gdcmValEntry* >(currentEntry);
+ valEntry = dynamic_cast< ValEntry* >(currentEntry);
if ( !valEntry ) // Euuuuh? It wasn't a ValEntry
// then we change it to a ValEntry ?
// Shouldn't it be considered as an error ?
{
- // We need to promote the gdcmDocEntry to a gdcmValEntry:
- valEntry = new gdcmValEntry(currentEntry);
+ // We need to promote the DocEntry to a ValEntry:
+ valEntry = new ValEntry(currentEntry);
if (!RemoveEntry(currentEntry))
{
- dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: removal"
+ dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: removal"
" of previous DocEntry failed.");
return NULL;
}
if ( !AddEntry(valEntry))
{
- dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: adding"
+ dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: adding"
" promoted ValEntry failed.");
return NULL;
}
/*
* \brief Modifies the value of a given Header Entry (Dicom Element)
* when it exists. Create it with the given value when unexistant.
- * @param voidArea (binary) value to be set
+ * @param binArea (binary) value to be set
* @param Group Group number of the Entry
* @param Elem Element number of the Entry
* \return pointer to the modified/created Header Entry (NULL when creation
* failed).
*/
-gdcmBinEntry * gdcmDocument::ReplaceOrCreateByNumber(
- void *voidArea,
+BinEntry* Document::ReplaceOrCreateByNumber(
+ uint8_t* binArea,
int lgth,
uint16_t group,
uint16_t elem,
- std::string const & VR )
+ std::string const& VR )
{
- gdcmBinEntry* binEntry = 0;
- gdcmDocEntry* currentEntry = GetDocEntryByNumber( group, elem);
+ BinEntry* binEntry = 0;
+ DocEntry* currentEntry = GetDocEntryByNumber( group, elem);
if (!currentEntry)
{
// check if (group,element) DictEntry exists
- // if it doesn't, create an entry in gdcmDictSet::VirtualEntry
+ // if it doesn't, create an entry in DictSet::VirtualEntry
// and use it
// Find out if the tag we received is in the dictionaries:
- gdcmDict *pubDict = gdcmGlobal::GetDicts()->GetDefaultPubDict();
- gdcmDictEntry *dictEntry = pubDict->GetDictEntryByNumber(group, elem);
+ Dict *pubDict = Global::GetDicts()->GetDefaultPubDict();
+ DictEntry *dictEntry = pubDict->GetDictEntryByNumber(group, elem);
if (!dictEntry)
{
}
if (!currentEntry)
{
- dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: call to"
+ dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: call to"
" NewDocEntryByNumber failed.");
return NULL;
}
- binEntry = new gdcmBinEntry(currentEntry);
+ binEntry = new BinEntry(currentEntry);
if ( !AddEntry(binEntry))
{
- dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: AddEntry"
+ dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: AddEntry"
" failed allthough this is a creation.");
}
}
else
{
- binEntry = dynamic_cast< gdcmBinEntry* >(currentEntry);
+ binEntry = dynamic_cast< BinEntry* >(currentEntry);
if ( !binEntry ) // Euuuuh? It wasn't a BinEntry
// then we change it to a BinEntry ?
// Shouldn't it be considered as an error ?
{
- // We need to promote the gdcmDocEntry to a gdcmBinEntry:
- binEntry = new gdcmBinEntry(currentEntry);
+ // We need to promote the DocEntry to a BinEntry:
+ binEntry = new BinEntry(currentEntry);
if (!RemoveEntry(currentEntry))
{
- dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: removal"
+ dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: removal"
" of previous DocEntry failed.");
return NULL;
}
if ( !AddEntry(binEntry))
{
- dbg.Verbose(0, "gdcmDocument::ReplaceOrCreateByNumber: adding"
+ dbg.Verbose(0, "Document::ReplaceOrCreateByNumber: adding"
" promoted BinEntry failed.");
return NULL;
}
}
}
- SetEntryByNumber(voidArea, lgth, group, elem);
+ SetEntryByNumber(binArea, lgth, group, elem);
return binEntry;
}
* \return pointer to the modified/created SeqEntry (NULL when creation
* failed).
*/
-gdcmSeqEntry * gdcmDocument::ReplaceOrCreateByNumber(
+SeqEntry* Document::ReplaceOrCreateByNumber(
uint16_t group,
uint16_t elem)
{
- gdcmSeqEntry* b = 0;
- gdcmDocEntry* a = GetDocEntryByNumber( group, elem);
+ SeqEntry* b = 0;
+ DocEntry* a = GetDocEntryByNumber( group, elem);
if (!a)
{
a = NewSeqEntryByNumber(group, elem);
return 0;
}
- b = new gdcmSeqEntry(a, 1); // FIXME : 1 (Depth)
+ b = new SeqEntry(a, 1); // FIXME : 1 (Depth)
AddEntry(b);
}
return b;
* @param elem element number of the Entry
* \return boolean
*/
-bool gdcmDocument::ReplaceIfExistByNumber(std::string const & value,
+bool Document::ReplaceIfExistByNumber(std::string const & value,
uint16_t group, uint16_t elem )
{
SetEntryByNumber(value, group, elem);
* @param element Element number of the searched Dicom Element
* @return true is found
*/
-bool gdcmDocument::CheckIfEntryExistByNumber(uint16_t group, uint16_t element )
+bool Document::CheckIfEntryExistByNumber(uint16_t group, uint16_t element )
{
- const std::string &key = gdcmDictEntry::TranslateToKey(group, element );
+ const std::string &key = DictEntry::TranslateToKey(group, element );
return TagHT.count(key);
}
* @return Corresponding element value when it exists,
* and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
*/
-std::string gdcmDocument::GetEntryByName(TagName const & tagName)
+std::string Document::GetEntryByName(TagName const& tagName)
{
- gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
+ DictEntry* dictEntry = RefPubDict->GetDictEntryByName(tagName);
if( !dictEntry )
{
return GDCM_UNFOUND;
* @return Corresponding element value representation when it exists,
* and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
*/
-std::string gdcmDocument::GetEntryVRByName(TagName const & tagName)
+std::string Document::GetEntryVRByName(TagName const& tagName)
{
- gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
+ DictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
if( dictEntry == NULL)
{
return GDCM_UNFOUND;
}
- gdcmDocEntry* elem = GetDocEntryByNumber(dictEntry->GetGroup(),
+ DocEntry* elem = GetDocEntryByNumber(dictEntry->GetGroup(),
dictEntry->GetElement());
return elem->GetVR();
}
* @return Corresponding element value representation when it exists,
* and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
*/
-std::string gdcmDocument::GetEntryByNumber(uint16_t group, uint16_t element)
+std::string Document::GetEntryByNumber(uint16_t group, uint16_t element)
{
- gdcmTagKey key = gdcmDictEntry::TranslateToKey(group, element);
+ TagKey key = DictEntry::TranslateToKey(group, element);
/// \todo use map methods, instead of multimap JPR
if ( !TagHT.count(key))
{
return GDCM_UNFOUND;
}
- return ((gdcmValEntry *)TagHT.find(key)->second)->GetValue();
+ return ((ValEntry *)TagHT.find(key)->second)->GetValue();
}
/**
* @return Corresponding element value representation when it exists,
* and the string GDCM_UNFOUND ("gdcm::Unfound") otherwise.
*/
-std::string gdcmDocument::GetEntryVRByNumber(uint16_t group, uint16_t element)
+std::string Document::GetEntryVRByNumber(uint16_t group, uint16_t element)
{
- gdcmDocEntry* elem = GetDocEntryByNumber(group, element);
+ DocEntry* elem = GetDocEntryByNumber(group, element);
if ( !elem )
{
return GDCM_UNFOUND;
* @param element Element number of the searched tag.
* @return Corresponding element length; -2 if not found
*/
-int gdcmDocument::GetEntryLengthByNumber(uint16_t group, uint16_t element)
+int Document::GetEntryLengthByNumber(uint16_t group, uint16_t element)
{
- gdcmDocEntry* elem = GetDocEntryByNumber(group, element);
+ DocEntry* elem = GetDocEntryByNumber(group, element);
if ( !elem )
{
return -2; //magic number
* @param tagName name of the searched Dicom Element.
* @return true when found
*/
-bool gdcmDocument::SetEntryByName(std::string const & content,std::string const & tagName)
+bool Document::SetEntryByName(std::string const & content,std::string const & tagName)
{
- gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
+ DictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
if( !dictEntry )
{
return false;
}
/**
- * \brief Accesses an existing gdcmDocEntry (i.e. a Dicom Element)
+ * \brief Accesses an existing DocEntry (i.e. a Dicom Element)
* through it's (group, element) and modifies it's content with
* the given value.
* @param content new value (string) to substitute with
* @param group group number of the Dicom Element to modify
* @param element element number of the Dicom Element to modify
*/
-bool gdcmDocument::SetEntryByNumber(std::string const & content,
+bool Document::SetEntryByNumber(std::string const& content,
uint16_t group,
uint16_t element)
{
int c;
int l;
- gdcmValEntry* valEntry = GetValEntryByNumber(group, element);
+ ValEntry* valEntry = GetValEntryByNumber(group, element);
if (!valEntry )
{
- dbg.Verbose(0, "gdcmDocument::SetEntryByNumber: no corresponding",
+ dbg.Verbose(0, "Document::SetEntryByNumber: no corresponding",
" ValEntry (try promotion first).");
return false;
}
l = finalContent.length();
if ( l != 0) // To avoid to be cheated by 'zero length' integers
{
- gdcmVRKey vr = valEntry->GetVR();
+ VRKey vr = valEntry->GetVR();
if( vr == "US" || vr == "SS" )
{
- c = CountSubstring(content, "\\") + 1; // for multivaluated items
+ // for multivaluated items
+ c = Util::CountSubstring(content, "\\") + 1;
l = c*2;
}
else if( vr == "UL" || vr == "SL" )
{
- c = CountSubstring(content, "\\") + 1; // for multivaluated items
+ // for multivaluated items
+ c = Util::CountSubstring(content, "\\") + 1;
l = c*4;;
}
}
}
/**
- * \brief Accesses an existing gdcmDocEntry (i.e. a Dicom Element)
+ * \brief Accesses an existing DocEntry (i.e. a Dicom Element)
* through it's (group, element) and modifies it's content with
* the given value.
- * @param content new value (void *) to substitute with
+ * @param content new value (void* -> uint8_t*) to substitute with
* @param lgth new value length
* @param group group number of the Dicom Element to modify
* @param element element number of the Dicom Element to modify
*/
-bool gdcmDocument::SetEntryByNumber(void *content,
+bool Document::SetEntryByNumber(uint8_t*content,
int lgth,
uint16_t group,
uint16_t element)
{
(void)lgth; //not used
- gdcmTagKey key = gdcmDictEntry::TranslateToKey(group, element);
+ TagKey key = DictEntry::TranslateToKey(group, element);
if ( !TagHT.count(key))
{
return false;
//content = content + '\0'; // fing a trick to enlarge a binary field?
}
*/
- gdcmBinEntry* a = (gdcmBinEntry *)TagHT[key];
- a->SetVoidArea(content);
+ BinEntry* a = (BinEntry *)TagHT[key];
+ a->SetBinArea(content);
a->SetLength(lgth);
a->SetValue(GDCM_BINLOADED);
}
/**
- * \brief Accesses an existing gdcmDocEntry (i.e. a Dicom Element)
+ * \brief Accesses an existing DocEntry (i.e. a Dicom Element)
* in the PubDocEntrySet of this instance
* through it's (group, element) and modifies it's length with
* the given value.
* @param element element number of the Entry to modify
* @return true on success, false otherwise.
*/
-bool gdcmDocument::SetEntryLengthByNumber(uint32_t l,
+bool Document::SetEntryLengthByNumber(uint32_t l,
uint16_t group,
uint16_t element)
{
/// \todo use map methods, instead of multimap JPR
- gdcmTagKey key = gdcmDictEntry::TranslateToKey(group, element);
+ TagKey key = DictEntry::TranslateToKey(group, element);
if ( !TagHT.count(key) )
{
return false;
* @param elem element number of the Entry
* @return File Offset of the Element Value
*/
-size_t gdcmDocument::GetEntryOffsetByNumber(uint16_t group, uint16_t elem)
+size_t Document::GetEntryOffsetByNumber(uint16_t group, uint16_t elem)
{
- gdcmDocEntry* entry = GetDocEntryByNumber(group, elem);
+ DocEntry* entry = GetDocEntryByNumber(group, elem);
if (!entry)
{
- dbg.Verbose(1, "gdcmDocument::GetDocEntryByNumber: no entry present.");
+ dbg.Verbose(1, "Document::GetDocEntryByNumber: no entry present.");
return 0;
}
return entry->GetOffset();
* @param elem element number of the Entry
* @return Pointer to the 'non string' area
*/
-void * gdcmDocument::GetEntryVoidAreaByNumber(uint16_t group, uint16_t elem)
+void* Document::GetEntryBinAreaByNumber(uint16_t group, uint16_t elem)
{
- gdcmDocEntry* entry = GetDocEntryByNumber(group, elem);
+ DocEntry* entry = GetDocEntryByNumber(group, elem);
if (!entry)
{
- dbg.Verbose(1, "gdcmDocument::GetDocEntryByNumber: no entry");
+ dbg.Verbose(1, "Document::GetDocEntryByNumber: no entry");
return 0;
}
- return ((gdcmBinEntry *)entry)->GetVoidArea();
+ if ( BinEntry* binEntry = dynamic_cast<BinEntry*>(entry) )
+ {
+ return binEntry->GetBinArea();
+ }
+
+ return 0;
}
/**
* @param group group number of the Entry
* @param elem element number of the Entry
*/
-void* gdcmDocument::LoadEntryVoidArea(uint16_t group, uint16_t elem)
+void* Document::LoadEntryBinArea(uint16_t group, uint16_t elem)
{
- gdcmDocEntry *docElement = GetDocEntryByNumber(group, elem);
+ DocEntry *docElement = GetDocEntryByNumber(group, elem);
if ( !docElement )
{
return NULL;
size_t o =(size_t)docElement->GetOffset();
fseek(Fp, o, SEEK_SET);
size_t l = docElement->GetLength();
- char* a = new char[l];
+ uint8_t* a = new uint8_t[l];
if(!a)
{
- dbg.Verbose(0, "gdcmDocument::LoadEntryVoidArea cannot allocate a");
+ dbg.Verbose(0, "Document::LoadEntryBinArea cannot allocate a");
return NULL;
}
size_t l2 = fread(a, 1, l , Fp);
return NULL;
}
/// \todo Drop any already existing void area! JPR
- if( !SetEntryVoidAreaByNumber( a, group, elem ) );
+ if( !SetEntryBinAreaByNumber( a, group, elem ) )
{
- dbg.Verbose(0, "gdcmDocument::LoadEntryVoidArea setting failed.");
+ dbg.Verbose(0, "Document::LoadEntryBinArea setting failed.");
}
return a;
}
/**
* \brief Loads (from disk) the element content
* when a string is not suitable
- * @param element Entry whose voidArea is going to be loaded
+ * @param element Entry whose binArea is going to be loaded
*/
-void *gdcmDocument::LoadEntryVoidArea(gdcmBinEntry *element)
+void* Document::LoadEntryBinArea(BinEntry* element)
{
size_t o =(size_t)element->GetOffset();
fseek(Fp, o, SEEK_SET);
size_t l = element->GetLength();
- char* a = new char[l];
+ uint8_t* a = new uint8_t[l];
if( !a )
{
- dbg.Verbose(0, "gdcmDocument::LoadEntryVoidArea cannot allocate a");
+ dbg.Verbose(0, "Document::LoadEntryBinArea cannot allocate a");
return NULL;
}
- element->SetVoidArea((void *)a);
+ element->SetBinArea((uint8_t*)a);
/// \todo check the result
size_t l2 = fread(a, 1, l , Fp);
if( l != l2 )
* @param element Element number of the searched Dicom Element
* @return
*/
-bool gdcmDocument::SetEntryVoidAreaByNumber(void * area,
+bool Document::SetEntryBinAreaByNumber(uint8_t* area,
uint16_t group,
uint16_t element)
{
- gdcmDocEntry* currentEntry = GetDocEntryByNumber(group, element);
+ DocEntry* currentEntry = GetDocEntryByNumber(group, element);
if ( !currentEntry )
{
return false;
}
- if ( gdcmBinEntry* binEntry = dynamic_cast<gdcmBinEntry*>(currentEntry) )
+ if ( BinEntry* binEntry = dynamic_cast<BinEntry*>(currentEntry) )
{
- binEntry->SetVoidArea( area );
+ binEntry->SetBinArea( area );
return true;
}
return true;
* \brief Update the entries with the shadow dictionary.
* Only non even entries are analyzed
*/
-void gdcmDocument::UpdateShaEntries()
+void Document::UpdateShaEntries()
{
- //gdcmDictEntry *entry;
+ //DictEntry *entry;
std::string vr;
/// \todo TODO : still any use to explore recursively the whole structure?
* @return Corresponding Dicom Element when it exists, and NULL
* otherwise.
*/
-gdcmDocEntry* gdcmDocument::GetDocEntryByName(std::string const & tagName)
+DocEntry* Document::GetDocEntryByName(std::string const & tagName)
{
- gdcmDictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
+ DictEntry *dictEntry = RefPubDict->GetDictEntryByName(tagName);
if( !dictEntry )
{
return NULL;
* @param element Element number of the searched Dicom Element
* @return
*/
-gdcmDocEntry* gdcmDocument::GetDocEntryByNumber(uint16_t group,
+DocEntry* Document::GetDocEntryByNumber(uint16_t group,
uint16_t element)
{
- gdcmTagKey key = gdcmDictEntry::TranslateToKey(group, element);
+ TagKey key = DictEntry::TranslateToKey(group, element);
if ( !TagHT.count(key))
{
return NULL;
}
/**
- * \brief Same as \ref gdcmDocument::GetDocEntryByNumber except it only
+ * \brief Same as \ref Document::GetDocEntryByNumber except it only
* returns a result when the corresponding entry is of type
* ValEntry.
* @return When present, the corresponding ValEntry.
*/
-gdcmValEntry* gdcmDocument::GetValEntryByNumber(uint16_t group,
+ValEntry* Document::GetValEntryByNumber(uint16_t group,
uint16_t element)
{
- gdcmDocEntry* currentEntry = GetDocEntryByNumber(group, element);
+ DocEntry* currentEntry = GetDocEntryByNumber(group, element);
if ( !currentEntry )
{
return 0;
}
- if ( gdcmValEntry* valEntry = dynamic_cast<gdcmValEntry*>(currentEntry) )
+ if ( ValEntry* valEntry = dynamic_cast<ValEntry*>(currentEntry) )
{
return valEntry;
}
- dbg.Verbose(0, "gdcmDocument::GetValEntryByNumber: unfound ValEntry.");
+ dbg.Verbose(0, "Document::GetValEntryByNumber: unfound ValEntry.");
return 0;
}
* @param entry Header Entry whose value shall be loaded.
* @return
*/
-void gdcmDocument::LoadDocEntrySafe(gdcmDocEntry * entry)
+void Document::LoadDocEntrySafe(DocEntry * entry)
{
long PositionOnEntry = ftell(Fp);
LoadDocEntry(entry);
* processor order.
* @return The properly swaped 32 bits integer.
*/
-uint32_t gdcmDocument::SwapLong(uint32_t a)
+uint32_t Document::SwapLong(uint32_t a)
{
switch (SwapCode)
{
break;
default :
//std::cout << "swapCode= " << SwapCode << std::endl;
- dbg.Error(" gdcmDocument::SwapLong : unset swap code");
+ dbg.Error(" Document::SwapLong : unset swap code");
a = 0;
}
return a;
* processor order.
* @return The properly unswaped 32 bits integer.
*/
-uint32_t gdcmDocument::UnswapLong(uint32_t a)
+uint32_t Document::UnswapLong(uint32_t a)
{
return SwapLong(a);
}
* \brief Swaps the bytes so they agree with the processor order
* @return The properly swaped 16 bits integer.
*/
-uint16_t gdcmDocument::SwapShort(uint16_t a)
+uint16_t Document::SwapShort(uint16_t a)
{
if ( SwapCode == 4321 || SwapCode == 2143 )
{
* \brief Unswaps the bytes so they agree with the processor order
* @return The properly unswaped 16 bits integer.
*/
-uint16_t gdcmDocument::UnswapShort(uint16_t a)
+uint16_t Document::UnswapShort(uint16_t a)
{
return SwapShort(a);
}
* \brief Parses a DocEntrySet (Zero-level DocEntries or SQ Item DocEntries)
* @return length of the parsed set.
*/
-
-long gdcmDocument::ParseDES(gdcmDocEntrySet *set,
+void Document::ParseDES(DocEntrySet *set,
long offset,
long l_max,
bool delim_mode)
{
- gdcmDocEntry *newDocEntry = 0;
- unsigned long l = 0;
+ DocEntry *newDocEntry = 0;
while (true)
{
break;
}
- gdcmVRKey vr = newDocEntry->GetVR();
+ VRKey vr = newDocEntry->GetVR();
if ( vr != "SQ" )
{
- if ( gdcmGlobal::GetVR()->IsVROfGdcmStringRepresentable(vr) )
+ if ( Global::GetVR()->IsVROfGdcmStringRepresentable(vr) )
{
/////////////////////// ValEntry
- gdcmValEntry* newValEntry =
- new gdcmValEntry( newDocEntry->GetDictEntry() );
+ ValEntry* newValEntry =
+ new ValEntry( newDocEntry->GetDictEntry() );
newValEntry->Copy( newDocEntry );
- // When "set" is a gdcmDocument, then we are at the top of the
+ // When "set" is a Document, then we are at the top of the
// hierarchy and the Key is simply of the form ( group, elem )...
- if (gdcmDocument* dummy = dynamic_cast< gdcmDocument* > ( set ) )
+ if (Document* dummy = dynamic_cast< Document* > ( set ) )
{
(void)dummy;
newValEntry->SetKey( newValEntry->GetKey() );
}
- // ...but when "set" is a gdcmSQItem, we are inserting this new
+ // ...but when "set" is a SQItem, we are inserting this new
// valEntry in a sequence item. Hence the key has the
- // generalized form (refer to \ref gdcmBaseTagKey):
- if (gdcmSQItem* parentSQItem = dynamic_cast< gdcmSQItem* > ( set ) )
+ // generalized form (refer to \ref BaseTagKey):
+ if (SQItem* parentSQItem = dynamic_cast< SQItem* > ( set ) )
{
newValEntry->SetKey( parentSQItem->GetBaseTagKey()
+ newValEntry->GetKey() );
}
else
{
- if ( ! gdcmGlobal::GetVR()->IsVROfGdcmBinaryRepresentable(vr) )
+ if ( ! Global::GetVR()->IsVROfGdcmBinaryRepresentable(vr) )
{
////// Neither ValEntry NOR BinEntry: should mean UNKOWN VR
- dbg.Verbose(0, "gdcmDocument::ParseDES: neither Valentry, "
+ dbg.Verbose(0, "Document::ParseDES: neither Valentry, "
"nor BinEntry. Probably unknown VR.");
}
//////////////////// BinEntry or UNKOWN VR:
- gdcmBinEntry* newBinEntry =
- new gdcmBinEntry( newDocEntry->GetDictEntry() );
+ BinEntry* newBinEntry =
+ new BinEntry( newDocEntry->GetDictEntry() );
newBinEntry->Copy( newDocEntry );
- // When "this" is a gdcmDocument the Key is simply of the
+ // When "this" is a Document the Key is simply of the
// form ( group, elem )...
- if (gdcmDocument* dummy = dynamic_cast< gdcmDocument* > ( set ) )
+ if (Document* dummy = dynamic_cast< Document* > ( set ) )
{
(void)dummy;
newBinEntry->SetKey( newBinEntry->GetKey() );
}
// but when "this" is a SQItem, we are inserting this new
// valEntry in a sequence item, and the kay has the
- // generalized form (refer to \ref gdcmBaseTagKey):
- if (gdcmSQItem* parentSQItem = dynamic_cast< gdcmSQItem* > ( set ) )
+ // generalized form (refer to \ref BaseTagKey):
+ if (SQItem* parentSQItem = dynamic_cast< SQItem* > ( set ) )
{
newBinEntry->SetKey( parentSQItem->GetBaseTagKey()
+ newBinEntry->GetKey() );
LoadDocEntry( newBinEntry );
}
- if (newDocEntry->GetGroup() == 0x7fe0 &&
- newDocEntry->GetElement() == 0x0010 )
+ if ( ( newDocEntry->GetGroup() == 0x7fe0 )
+ && ( newDocEntry->GetElement() == 0x0010 ) )
{
- if (newDocEntry->GetReadLength()==0xffffffff)
+ if ( IsRLELossLessTransferSyntax() )
{
- // Broken US.3405.1.dcm
- Parse7FE0(); // to skip the pixels
- // (multipart JPEG/RLE are trouble makers)
+ long PositionOnEntry = ftell(Fp);
+ fseek( Fp, newDocEntry->GetOffset(), SEEK_SET );
+ ComputeRLEInfo();
+ fseek( Fp, PositionOnEntry, SEEK_SET );
}
- else
+ else
+ if ( IsJPEGTransferSyntax() )
{
- SkipToNextDocEntry(newDocEntry);
- l = newDocEntry->GetFullLength();
+ long PositionOnEntry = ftell(Fp);
+ fseek( Fp, newDocEntry->GetOffset(), SEEK_SET );
+ ComputeJPEGFragmentInfo();
+ fseek( Fp, PositionOnEntry, SEEK_SET );
}
}
- else
- {
- // to be sure we are at the beginning
- SkipToNextDocEntry(newDocEntry);
- l = newDocEntry->GetFullLength();
- }
+
+ // Just to make sure we are at the beginning of next entry.
+ SkipToNextDocEntry(newDocEntry);
}
else
{
// VR = "SQ"
- l = newDocEntry->GetReadLength();
+ unsigned long l = newDocEntry->GetReadLength();
if ( l != 0 ) // don't mess the delim_mode for zero-length sequence
{
if ( l == 0xffffffff )
}
}
// no other way to create it ...
- gdcmSeqEntry* newSeqEntry =
- new gdcmSeqEntry( newDocEntry->GetDictEntry() );
+ SeqEntry* newSeqEntry =
+ new SeqEntry( newDocEntry->GetDictEntry() );
newSeqEntry->Copy( newDocEntry );
newSeqEntry->SetDelimitorMode( delim_mode );
- // At the top of the hierarchy, stands a gdcmDocument. When "set"
- // is a gdcmDocument, then we are building the first depth level.
- // Hence the gdcmSeqEntry we are building simply has a depth
+ // At the top of the hierarchy, stands a Document. When "set"
+ // is a Document, then we are building the first depth level.
+ // Hence the SeqEntry we are building simply has a depth
// level of one:
- if (gdcmDocument* dummy = dynamic_cast< gdcmDocument* > ( set ) )
+ if (Document* dummy = dynamic_cast< Document* > ( set ) )
{
(void)dummy;
newSeqEntry->SetDepthLevel( 1 );
newSeqEntry->SetKey( newSeqEntry->GetKey() );
}
// But when "set" is allready a SQItem, we are building a nested
- // sequence, and hence the depth level of the new gdcmSeqEntry
+ // sequence, and hence the depth level of the new SeqEntry
// we are building, is one level deeper:
- if (gdcmSQItem* parentSQItem = dynamic_cast< gdcmSQItem* > ( set ) )
+ if (SQItem* parentSQItem = dynamic_cast< SQItem* > ( set ) )
{
newSeqEntry->SetDepthLevel( parentSQItem->GetDepthLevel() + 1 );
newSeqEntry->SetKey( parentSQItem->GetBaseTagKey()
if ( l != 0 )
{ // Don't try to parse zero-length sequences
- (void)ParseSQ( newSeqEntry,
- newDocEntry->GetOffset(),
- l, delim_mode);
+ ParseSQ( newSeqEntry,
+ newDocEntry->GetOffset(),
+ l, delim_mode);
}
set->AddEntry( newSeqEntry );
if ( !delim_mode && (ftell(Fp)-offset) >= l_max)
}
delete newDocEntry;
}
- return l; // Probably useless
}
/**
* \brief Parses a Sequence ( SeqEntry after SeqEntry)
* @return parsed length for this level
*/
-long gdcmDocument::ParseSQ( gdcmSeqEntry* seqEntry,
+void Document::ParseSQ( SeqEntry* seqEntry,
long offset, long l_max, bool delim_mode)
{
int SQItemNumber = 0;
while (true)
{
- gdcmDocEntry* newDocEntry = ReadNextDocEntry();
+ DocEntry* newDocEntry = ReadNextDocEntry();
if ( !newDocEntry )
{
// FIXME Should warn user
break;
}
- gdcmSQItem *itemSQ = new gdcmSQItem( seqEntry->GetDepthLevel() );
+ SQItem *itemSQ = new SQItem( seqEntry->GetDepthLevel() );
std::ostringstream newBase;
newBase << seqEntry->GetKey()
<< "/"
dlm_mod = false;
}
- (void)ParseDES(itemSQ, newDocEntry->GetOffset(), l, dlm_mod);
+ ParseDES(itemSQ, newDocEntry->GetOffset(), l, dlm_mod);
seqEntry->AddEntry( itemSQ, SQItemNumber );
SQItemNumber++;
break;
}
}
-
- int lgth = ftell(Fp) - offset;
- return lgth;
}
/**
* \brief Loads the element content if its length doesn't exceed
- * the value specified with gdcmDocument::SetMaxSizeLoadEntry()
+ * the value specified with Document::SetMaxSizeLoadEntry()
* @param entry Header Entry (Dicom Element) to be dealt with
*/
-void gdcmDocument::LoadDocEntry(gdcmDocEntry* entry)
+void Document::LoadDocEntry(DocEntry* entry)
{
size_t item_read;
uint16_t group = entry->GetGroup();
// When the length is zero things are easy:
if ( length == 0 )
{
- ((gdcmValEntry *)entry)->SetValue("");
+ ((ValEntry *)entry)->SetValue("");
return;
}
std::ostringstream s;
if (length > MaxSizeLoadEntry)
{
- if (gdcmBinEntry* binEntryPtr = dynamic_cast< gdcmBinEntry* >(entry) )
+ if (BinEntry* binEntryPtr = dynamic_cast< BinEntry* >(entry) )
{
//s << "gdcm::NotLoaded (BinEntry)";
s << GDCM_NOTLOADED;
binEntryPtr->SetValue(s.str());
}
// Be carefull : a BinEntry IS_A ValEntry ...
- else if (gdcmValEntry* valEntryPtr = dynamic_cast< gdcmValEntry* >(entry) )
+ else if (ValEntry* valEntryPtr = dynamic_cast< ValEntry* >(entry) )
{
// s << "gdcm::NotLoaded. (ValEntry)";
s << GDCM_NOTLOADED;
}
// When we find a BinEntry not very much can be done :
- if (gdcmBinEntry* binEntryPtr = dynamic_cast< gdcmBinEntry* >(entry) )
+ if (BinEntry* binEntryPtr = dynamic_cast< BinEntry* >(entry) )
{
s << GDCM_BINLOADED;
binEntryPtr->SetValue(s.str());
- LoadEntryVoidArea(binEntryPtr); // last one, not to erase length !
+ LoadEntryBinArea(binEntryPtr); // last one, not to erase length !
return;
}
s << std::ends; // to avoid oddities on Solaris
#endif //GDCM_NO_ANSI_STRING_STREAM
- ((gdcmValEntry *)entry)->SetValue(s.str());
+ ((ValEntry *)entry)->SetValue(s.str());
return;
}
str[length] = '\0';
std::string newValue = str;
delete[] str;
- if ( gdcmValEntry* valEntry = dynamic_cast<gdcmValEntry* >(entry) )
+ if ( ValEntry* valEntry = dynamic_cast<ValEntry* >(entry) )
{
if ( item_read != 1 )
{
- dbg.Verbose(1, "gdcmDocument::LoadDocEntry",
+ dbg.Verbose(1, "Document::LoadDocEntry",
"unread element value");
valEntry->SetValue(GDCM_UNREAD);
return;
}
else
{
- dbg.Error(true, "gdcmDocument::LoadDocEntry"
+ dbg.Error(true, "Document::LoadDocEntry"
"Should have a ValEntry, here !");
}
}
* \brief Find the value Length of the passed Header Entry
* @param entry Header Entry whose length of the value shall be loaded.
*/
-void gdcmDocument::FindDocEntryLength( gdcmDocEntry *entry )
- throw ( gdcmFormatError )
+void Document::FindDocEntryLength( DocEntry *entry )
+ throw ( FormatError )
{
uint16_t element = entry->GetElement();
std::string vr = entry->GetVR();
uint16_t length16;
- if ( Filetype == gdcmExplicitVR && !entry->IsImplicitVR() )
+ if ( Filetype == ExplicitVR && !entry->IsImplicitVR() )
{
if ( vr == "OB" || vr == "OW" || vr == "SQ" || vr == "UN" )
{
- // The following reserved two bytes (see PS 3.5-2001, section
- // 7.1.2 Data element structure with explicit vr p27) must be
+ // The following reserved two bytes (see PS 3.5-2003, section
+ // "7.1.2 Data element structure with explicit vr", p 27) must be
// skipped before proceeding on reading the length on 4 bytes.
fseek(Fp, 2L, SEEK_CUR);
uint32_t length32 = ReadInt32();
- if ( vr == "OB" && length32 == 0xffffffff )
+ if ( (vr == "OB" || vr == "OW") && length32 == 0xffffffff )
{
uint32_t lengthOB;
try
{
+ /// \todo rename that to FindDocEntryLengthOBOrOW since
+ /// the above test is on both OB and OW...
lengthOB = FindDocEntryLengthOB();
}
- catch ( gdcmFormatUnexpected )
+ catch ( FormatUnexpected )
{
// Computing the length failed (this happens with broken
// files like gdcm-JPEG-LossLess3a.dcm). We still have a
{
if ( !IsExplicitVRBigEndianTransferSyntax() )
{
- throw gdcmFormatError( "gdcmDocument::FindDocEntryLength()",
- " not explicit VR." );
+ throw FormatError( "Document::FindDocEntryLength()",
+ " not explicit VR." );
return;
}
length16 = 4;
// and the dictionary entry depending on them.
uint16_t correctGroup = SwapShort( entry->GetGroup() );
uint16_t correctElem = SwapShort( entry->GetElement() );
- gdcmDictEntry* newTag = GetDictEntryByNumber( correctGroup,
+ DictEntry* newTag = GetDictEntryByNumber( correctGroup,
correctElem );
if ( !newTag )
{
* \brief Find the Value Representation of the current Dicom Element.
* @param entry
*/
-void gdcmDocument::FindDocEntryVR( gdcmDocEntry *entry )
+void Document::FindDocEntryVR( DocEntry *entry )
{
- if ( Filetype != gdcmExplicitVR )
+ if ( Filetype != ExplicitVR )
{
return;
}
* @return false if the VR is incorrect of if the VR isn't referenced
* otherwise, it returns true
*/
-bool gdcmDocument::CheckDocEntryVR(gdcmDocEntry *entry, gdcmVRKey vr)
+bool Document::CheckDocEntryVR(DocEntry *entry, VRKey vr)
{
- char msg[100]; // for sprintf
+ std::string msg;
bool realExplicit = true;
// Assume we are reading a falsely explicit VR file i.e. we reached
// CLEANME searching the dicom_vr at each occurence is expensive.
// PostPone this test in an optional integrity check at the end
// of parsing or only in debug mode.
- if ( realExplicit && !gdcmGlobal::GetVR()->Count(vr) )
+ if ( realExplicit && !Global::GetVR()->Count(vr) )
{
realExplicit = false;
}
{
// We thought this was explicit VR, but we end up with an
// implicit VR tag. Let's backtrack.
- sprintf(msg,"Falsely explicit vr file (%04x,%04x)\n",
- entry->GetGroup(), entry->GetElement());
- dbg.Verbose(1, "gdcmDocument::FindVR: ",msg);
+ msg = Util::Format("Falsely explicit vr file (%04x,%04x)\n",
+ entry->GetGroup(), entry->GetElement());
+ dbg.Verbose(1, "Document::FindVR: ", msg.c_str());
if( entry->GetGroup() % 2 && entry->GetElement() == 0x0000)
{
// Group length is UL !
- gdcmDictEntry* newEntry = NewVirtualDictEntry(
+ DictEntry* newEntry = NewVirtualDictEntry(
entry->GetGroup(), entry->GetElement(),
"UL", "FIXME", "Group Length");
entry->SetDictEntry( newEntry );
// be unwise to overwrite the VR of a dictionary (since it would
// compromise it's next user), we need to clone the actual DictEntry
// and change the VR for the read one.
- gdcmDictEntry* newEntry = NewVirtualDictEntry(
+ DictEntry* newEntry = NewVirtualDictEntry(
entry->GetGroup(), entry->GetElement(),
vr, "FIXME", entry->GetName());
entry->SetDictEntry(newEntry);
* @param entry entry to tranform
* @return Transformed entry value
*/
-std::string gdcmDocument::GetDocEntryValue(gdcmDocEntry *entry)
+std::string Document::GetDocEntryValue(DocEntry *entry)
{
if ( IsDocEntryAnInteger(entry) && entry->IsImplicitVR() )
{
- std::string val = ((gdcmValEntry *)entry)->GetValue();
+ std::string val = ((ValEntry *)entry)->GetValue();
std::string vr = entry->GetVR();
uint32_t length = entry->GetLength();
std::ostringstream s;
return s.str();
}
- return ((gdcmValEntry *)entry)->GetValue();
+ return ((ValEntry *)entry)->GetValue();
}
/**
* @param entry Entry to reverse transform
* @return Reverse transformed entry value
*/
-std::string gdcmDocument::GetDocEntryUnvalue(gdcmDocEntry* entry)
+std::string Document::GetDocEntryUnvalue(DocEntry* entry)
{
if ( IsDocEntryAnInteger(entry) && entry->IsImplicitVR() )
{
uint16_t newInt16;
tokens.erase( tokens.begin(), tokens.end()); // clean any previous value
- Tokenize (((gdcmValEntry *)entry)->GetValue(), tokens, "\\");
+ Util::Tokenize (((ValEntry *)entry)->GetValue(), tokens, "\\");
for (unsigned int i=0; i<tokens.size(); i++)
{
newInt16 = atoi(tokens[i].c_str());
uint32_t newInt32;
tokens.erase(tokens.begin(),tokens.end()); // clean any previous value
- Tokenize (((gdcmValEntry *)entry)->GetValue(), tokens, "\\");
+ Util::Tokenize (((ValEntry *)entry)->GetValue(), tokens, "\\");
for (unsigned int i=0; i<tokens.size();i++)
{
newInt32 = atoi(tokens[i].c_str());
return s.str();
}
- return ((gdcmValEntry *)entry)->GetValue();
+ return ((ValEntry *)entry)->GetValue();
}
/**
* \warning NOT end user intended method !
* @param entry entry to skip
*/
-void gdcmDocument::SkipDocEntry(gdcmDocEntry *entry)
+void Document::SkipDocEntry(DocEntry *entry)
{
SkipBytes(entry->GetLength());
}
* \warning NOT end user intended method !
* @param entry entry to skip
*/
-void gdcmDocument::SkipToNextDocEntry(gdcmDocEntry *entry)
+void Document::SkipToNextDocEntry(DocEntry *entry)
{
fseek(Fp, (long)(entry->GetOffset()), SEEK_SET);
fseek(Fp, (long)(entry->GetReadLength()), SEEK_CUR);
* @param entry entry to check
* @param foundLength fist assumption about length
*/
-void gdcmDocument::FixDocEntryFoundLength(gdcmDocEntry *entry,
+void Document::FixDocEntryFoundLength(DocEntry *entry,
uint32_t foundLength)
{
entry->SetReadLength( foundLength ); // will be updated only if a bug is found
* @param entry The element value on which to apply the predicate.
* @return The result of the heuristical predicate.
*/
-bool gdcmDocument::IsDocEntryAnInteger(gdcmDocEntry *entry)
+bool Document::IsDocEntryAnInteger(DocEntry *entry)
{
uint16_t element = entry->GetElement();
uint16_t group = entry->GetGroup();
// encounter such an ill-formed image, we simply display a warning
// message and proceed on parsing (while crossing fingers).
std::ostringstream s;
- int filePosition = ftell(Fp);
+ long filePosition = ftell(Fp);
s << "Erroneous Group Length element length on : (" \
<< std::hex << group << " , " << element
<< ") -before- position x(" << filePosition << ")"
<< "lgt : " << length;
- dbg.Verbose(0, "gdcmDocument::IsDocEntryAnInteger", s.str().c_str() );
+ dbg.Verbose(0, "Document::IsDocEntryAnInteger", s.str().c_str() );
}
}
* @return
*/
-uint32_t gdcmDocument::FindDocEntryLengthOB()
- throw( gdcmFormatUnexpected )
+uint32_t Document::FindDocEntryLengthOB()
+ throw( FormatUnexpected )
{
// See PS 3.5-2001, section A.4 p. 49 on encapsulation of encoded pixel data.
long positionOnEntry = ftell(Fp);
group = ReadInt16();
elem = ReadInt16();
}
- catch ( gdcmFormatError )
+ catch ( FormatError )
{
- throw gdcmFormatError("gdcmDocument::FindDocEntryLengthOB()",
- " group or element not present.");
+ throw FormatError("Document::FindDocEntryLengthOB()",
+ " group or element not present.");
}
// We have to decount the group and element we just read
if ( group != 0xfffe || ( ( elem != 0xe0dd ) && ( elem != 0xe000 ) ) )
{
- dbg.Verbose(1, "gdcmDocument::FindDocEntryLengthOB: neither an Item "
+ dbg.Verbose(1, "Document::FindDocEntryLengthOB: neither an Item "
"tag nor a Sequence delimiter tag.");
fseek(Fp, positionOnEntry, SEEK_SET);
- throw gdcmFormatUnexpected("gdcmDocument::FindDocEntryLengthOB()",
- "Neither an Item tag nor a Sequence "
- "delimiter tag.");
+ throw FormatUnexpected("Document::FindDocEntryLengthOB()",
+ "Neither an Item tag nor a Sequence "
+ "delimiter tag.");
}
if ( elem == 0xe0dd )
* (swaps it depending on processor endianity)
* @return read value
*/
-uint16_t gdcmDocument::ReadInt16()
- throw( gdcmFormatError )
+uint16_t Document::ReadInt16()
+ throw( FormatError )
{
uint16_t g;
size_t item_read = fread (&g, (size_t)2,(size_t)1, Fp);
{
if( ferror(Fp) )
{
- throw gdcmFormatError( "gdcmDocument::ReadInt16()", " file error." );
+ throw FormatError( "Document::ReadInt16()", " file error." );
}
- throw gdcmFormatError( "gdcmDocument::ReadInt16()", "EOF." );
+ throw FormatError( "Document::ReadInt16()", "EOF." );
}
g = SwapShort(g);
return g;
* (swaps it depending on processor endianity)
* @return read value
*/
-uint32_t gdcmDocument::ReadInt32()
- throw( gdcmFormatError )
+uint32_t Document::ReadInt32()
+ throw( FormatError )
{
uint32_t g;
size_t item_read = fread (&g, (size_t)4,(size_t)1, Fp);
{
if( ferror(Fp) )
{
- throw gdcmFormatError( "gdcmDocument::ReadInt16()", " file error." );
+ throw FormatError( "Document::ReadInt16()", " file error." );
}
- throw gdcmFormatError( "gdcmDocument::ReadInt32()", "EOF." );
+ throw FormatError( "Document::ReadInt32()", "EOF." );
}
g = SwapLong(g);
return g;
* \warning NOT end user intended method !
* @return
*/
-void gdcmDocument::SkipBytes(uint32_t nBytes)
+void Document::SkipBytes(uint32_t nBytes)
{
//FIXME don't dump the returned value
(void)fseek(Fp, (long)nBytes, SEEK_CUR);
* \brief Loads all the needed Dictionaries
* \warning NOT end user intended method !
*/
-void gdcmDocument::Initialise()
+void Document::Initialise()
{
- RefPubDict = gdcmGlobal::GetDicts()->GetDefaultPubDict();
+ RefPubDict = Global::GetDicts()->GetDefaultPubDict();
RefShaDict = NULL;
+ RLEInfo = new RLEFramesInfo;
+ JPEGInfo = new JPEGFragmentsInfo;
}
/**
* it's neither ACR-NEMA nor DICOM
* true when we hope ours assuptions are OK
*/
-bool gdcmDocument::CheckSwap()
+bool Document::CheckSwap()
{
// The only guaranted way of finding the swap code is to find a
// group tag since we know it's length has to be of four bytes i.e.
char *entCur = deb + 128;
if( memcmp(entCur, "DICM", (size_t)4) == 0 )
{
- dbg.Verbose(1, "gdcmDocument::CheckSwap:", "looks like DICOM Version3");
+ dbg.Verbose(1, "Document::CheckSwap:", "looks like DICOM Version3");
// Next, determine the value representation (VR). Let's skip to the
// first element (0002, 0000) and check there if we find "UL"
memcmp(entCur, "CS", (size_t)2) == 0 ) // CS, to remove later
// when Write DCM *adds*
// FIXME
- // Use gdcmDocument::dicom_vr to test all the possibilities
+ // Use Document::dicom_vr to test all the possibilities
// instead of just checking for UL, OB and UI !? group 0000
{
- Filetype = gdcmExplicitVR;
- dbg.Verbose(1, "gdcmDocument::CheckSwap:",
+ Filetype = ExplicitVR;
+ dbg.Verbose(1, "Document::CheckSwap:",
"explicit Value Representation");
}
else
{
- Filetype = gdcmImplicitVR;
- dbg.Verbose(1, "gdcmDocument::CheckSwap:",
+ Filetype = ImplicitVR;
+ dbg.Verbose(1, "Document::CheckSwap:",
"not an explicit Value Representation");
}
if ( net2host )
{
SwapCode = 4321;
- dbg.Verbose(1, "gdcmDocument::CheckSwap:",
+ dbg.Verbose(1, "Document::CheckSwap:",
"HostByteOrder != NetworkByteOrder");
}
else
{
SwapCode = 0;
- dbg.Verbose(1, "gdcmDocument::CheckSwap:",
+ dbg.Verbose(1, "Document::CheckSwap:",
"HostByteOrder = NetworkByteOrder");
}
// Alas, this is not a DicomV3 file and whatever happens there is no file
// preamble. We can reset the file position indicator to where the data
// is (i.e. the beginning of the file).
- dbg.Verbose(1, "gdcmDocument::CheckSwap:", "not a DICOM Version3 file");
+ dbg.Verbose(1, "Document::CheckSwap:", "not a DICOM Version3 file");
rewind(Fp);
// Our next best chance would be to be considering a 'clean' ACR/NEMA file.
{
case 0x00040000 :
SwapCode = 3412;
- Filetype = gdcmACR;
+ Filetype = ACR;
return true;
case 0x04000000 :
SwapCode = 4321;
- Filetype = gdcmACR;
+ Filetype = ACR;
return true;
case 0x00000400 :
SwapCode = 2143;
- Filetype = gdcmACR;
+ Filetype = ACR;
return true;
case 0x00000004 :
SwapCode = 0;
- Filetype = gdcmACR;
+ Filetype = ACR;
return true;
default :
// We are out of luck. It is not a DicomV3 nor a 'clean' ACR/NEMA file.
case 0x0004 :
case 0x0008 :
SwapCode = 0;
- Filetype = gdcmACR;
+ Filetype = ACR;
return true;
case 0x0200 :
case 0x0400 :
case 0x0800 :
SwapCode = 4321;
- Filetype = gdcmACR;
+ Filetype = ACR;
return true;
default :
- dbg.Verbose(0, "gdcmDocument::CheckSwap:",
+ dbg.Verbose(0, "Document::CheckSwap:",
"ACR/NEMA unfound swap info (Really hopeless !)");
- Filetype = gdcmUnknown;
+ Filetype = Unknown;
return false;
}
// Then the only info we have is the net2host one.
* \brief Restore the unproperly loaded values i.e. the group, the element
* and the dictionary entry depending on them.
*/
-void gdcmDocument::SwitchSwapToBigEndian()
+void Document::SwitchSwapToBigEndian()
{
- dbg.Verbose(1, "gdcmDocument::SwitchSwapToBigEndian",
+ dbg.Verbose(1, "Document::SwitchSwapToBigEndian",
"Switching to BigEndian mode.");
if ( SwapCode == 0 )
{
* \brief during parsing, Header Elements too long are not loaded in memory
* @param newSize
*/
-void gdcmDocument::SetMaxSizeLoadEntry(long newSize)
+void Document::SetMaxSizeLoadEntry(long newSize)
{
if ( newSize < 0 )
{
/**
* \brief Header Elements too long will not be printed
- * \todo See comments of \ref gdcmDocument::MAX_SIZE_PRINT_ELEMENT_VALUE
+ * \todo See comments of \ref Document::MAX_SIZE_PRINT_ELEMENT_VALUE
* @param newSize
*/
-void gdcmDocument::SetMaxSizePrintEntry(long newSize)
+void Document::SetMaxSizePrintEntry(long newSize)
{
//DOH !! This is exactly SetMaxSizeLoadEntry FIXME FIXME
if ( newSize < 0 )
* gets the VR, gets the length, gets the offset value)
* @return On succes the newly created DocEntry, NULL on failure.
*/
-gdcmDocEntry* gdcmDocument::ReadNextDocEntry()
+DocEntry* Document::ReadNextDocEntry()
{
uint16_t group;
uint16_t elem;
group = ReadInt16();
elem = ReadInt16();
}
- catch ( gdcmFormatError e )
+ catch ( FormatError e )
{
// We reached the EOF (or an error occured) therefore
// header parsing has to be considered as finished.
return 0;
}
- gdcmDocEntry *newEntry = NewDocEntryByNumber(group, elem);
+ DocEntry *newEntry = NewDocEntryByNumber(group, elem);
FindDocEntryVR(newEntry);
try
{
FindDocEntryLength(newEntry);
}
- catch ( gdcmFormatError e )
+ catch ( FormatError e )
{
// Call it quits
//std::cout << e;
/**
- * \brief Generate a free gdcmTagKey i.e. a gdcmTagKey that is not present
+ * \brief Generate a free TagKey i.e. a TagKey that is not present
* in the TagHt dictionary.
* @param group The generated tag must belong to this group.
* @return The element of tag with given group which is fee.
*/
-uint32_t gdcmDocument::GenerateFreeTagKeyInGroup(uint16_t group)
+uint32_t Document::GenerateFreeTagKeyInGroup(uint16_t group)
{
for (uint32_t elem = 0; elem < UINT32_MAX; elem++)
{
- gdcmTagKey key = gdcmDictEntry::TranslateToKey(group, elem);
+ TagKey key = DictEntry::TranslateToKey(group, elem);
if (TagHT.count(key) == 0)
{
return elem;
}
/**
- * \brief Assuming the internal file pointer \ref gdcmDocument::Fp
+ * \brief Assuming the internal file pointer \ref Document::Fp
* is placed at the beginning of a tag check whether this
* tag is (TestGroup, TestElement).
- * \warning On success the internal file pointer \ref gdcmDocument::Fp
+ * \warning On success the internal file pointer \ref Document::Fp
* is modified to point after the tag.
* On failure (i.e. when the tag wasn't the expected tag
* (TestGroup, TestElement) the internal file pointer
- * \ref gdcmDocument::Fp is restored to it's original position.
+ * \ref Document::Fp is restored to it's original position.
* @param testGroup The expected group of the tag.
* @param testElement The expected Element of the tag.
* @return True on success, false otherwise.
*/
-bool gdcmDocument::ReadTag(uint16_t testGroup, uint16_t testElement)
+bool Document::ReadTag(uint16_t testGroup, uint16_t testElement)
{
long positionOnEntry = ftell(Fp);
long currentPosition = ftell(Fp); // On debugging purposes
s << std::hex << itemTagGroup << "," << itemTagElement << ")"
<< std::endl;
s << " at address: " << (unsigned)currentPosition << std::endl;
- dbg.Verbose(0, "gdcmDocument::ReadItemTagLength: wrong Item Tag found:");
+ dbg.Verbose(0, "Document::ReadItemTagLength: wrong Item Tag found:");
dbg.Verbose(0, s.str().c_str());
fseek(Fp, positionOnEntry, SEEK_SET);
}
/**
- * \brief Assuming the internal file pointer \ref gdcmDocument::Fp
+ * \brief Assuming the internal file pointer \ref Document::Fp
* is placed at the beginning of a tag (TestGroup, TestElement),
* read the length associated to the Tag.
- * \warning On success the internal file pointer \ref gdcmDocument::Fp
+ * \warning On success the internal file pointer \ref Document::Fp
* is modified to point after the tag and it's length.
* On failure (i.e. when the tag wasn't the expected tag
* (TestGroup, TestElement) the internal file pointer
- * \ref gdcmDocument::Fp is restored to it's original position.
+ * \ref Document::Fp is restored to it's original position.
* @param testGroup The expected group of the tag.
* @param testElement The expected Element of the tag.
* @return On success returns the length associated to the tag. On failure
* returns 0.
*/
-uint32_t gdcmDocument::ReadTagLength(uint16_t testGroup, uint16_t testElement)
+uint32_t Document::ReadTagLength(uint16_t testGroup, uint16_t testElement)
{
long positionOnEntry = ftell(Fp);
(void)positionOnEntry;
s << "Basic Item Length is: "
<< itemLength << std::endl;
s << " at address: " << (unsigned)currentPosition << std::endl;
- dbg.Verbose(0, "gdcmDocument::ReadItemTagLength: ", s.str().c_str());
+ dbg.Verbose(0, "Document::ReadItemTagLength: ", s.str().c_str());
}
return itemLength;
}
/**
- * \brief Parse pixel data from disk for multi-fragment Jpeg/Rle files
- * No other way so 'skip' the Data
+ * \brief When parsing the Pixel Data of an encapsulated file, read
+ * the basic offset table (when present, and BTW dump it).
*/
-void gdcmDocument::Parse7FE0 ()
+void Document::ReadAndSkipEncapsulatedBasicOffsetTable()
{
- gdcmDocEntry* element = GetDocEntryByNumber(0x0002, 0x0010);
- if ( !element )
- {
- // Should warn user FIXME
- return;
- }
-
- if ( IsImplicitVRLittleEndianTransferSyntax()
- || IsExplicitVRLittleEndianTransferSyntax()
- || IsExplicitVRBigEndianTransferSyntax() /// \todo 1.2.2 ??? A verifier !
- || IsDeflatedExplicitVRLittleEndianTransferSyntax() )
- {
- return;
- }
-
- // ---------------- for Parsing : Position on begining of Jpeg/RLE Pixels
-
//// Read the Basic Offset Table Item Tag length...
uint32_t itemLength = ReadTagLength(0xfffe, 0xe000);
- //// ... and then read length[s] itself[themselves]. We don't use
- // the values read (BTW what is the purpous of those lengths ?)
+ // When present, read the basic offset table itself.
+ // Notes: - since the presence of this basic offset table is optional
+ // we can't rely on it for the implementation, and we will simply
+ // trash it's content (when present).
+ // - still, when present, we could add some further checks on the
+ // lengths, but we won't bother with such fuses for the time being.
if ( itemLength != 0 )
{
- // BTW, what is the purpous of those length anyhow !?
char* basicOffsetTableItemValue = new char[itemLength + 1];
fread(basicOffsetTableItemValue, itemLength, 1, Fp);
+#ifdef GDCM_DEBUG
for (unsigned int i=0; i < itemLength; i += 4 )
{
- uint32_t individualLength = str2num(&basicOffsetTableItemValue[i],uint32_t);
+ uint32_t individualLength = str2num( &basicOffsetTableItemValue[i],
+ uint32_t);
std::ostringstream s;
s << " Read one length: ";
s << std::hex << individualLength << std::endl;
- dbg.Verbose(0, "gdcmDocument::Parse7FE0: ", s.str().c_str());
+ dbg.Verbose(0,
+ "Document::ReadAndSkipEncapsulatedBasicOffsetTable: ",
+ s.str().c_str());
}
+#endif //GDCM_DEBUG
+
delete[] basicOffsetTableItemValue;
}
+}
+/**
+ * \brief Parse pixel data from disk of [multi-]fragment RLE encoding.
+ * Compute the RLE extra information and store it in \ref RLEInfo
+ * for later pixel retrieval usage.
+ */
+void Document::ComputeRLEInfo()
+{
if ( ! IsRLELossLessTransferSyntax() )
{
- // JPEG Image
-
- //// We then skip (not reading them) all the fragments of images:
- while ( (itemLength = ReadTagLength(0xfffe, 0xe000)) )
- {
- SkipBytes(itemLength);
- }
+ return;
}
- else
- {
- // RLE Image
- long ftellRes;
- long rleSegmentLength[15], fragmentLength;
- // While we find some items:
- while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) )
- {
- // Parse fragments of the current Fragment (Frame)
- //------------------ scanning (not reading) fragment pixels
- uint32_t nbRleSegments = ReadInt32();
+ // Encoded pixel data: for the time being we are only concerned with
+ // Jpeg or RLE Pixel data encodings.
+ // As stated in PS 3.5-2003, section 8.2 p44:
+ // "If sent in Encapsulated Format (i.e. other than the Native Format) the
+ // value representation OB is used".
+ // Hence we expect an OB value representation. Concerning OB VR,
+ // the section PS 3.5-2003, section A.4.c p 58-59, states:
+ // "For the Value Representations OB and OW, the encoding shall meet the
+ // following specifications depending on the Data element tag:"
+ // [...snip...]
+ // - the first item in the sequence of items before the encoded pixel
+ // data stream shall be basic offset table item. The basic offset table
+ // item value, however, is not required to be present"
+
+ ReadAndSkipEncapsulatedBasicOffsetTable();
+
+ // Encapsulated RLE Compressed Images (see PS 3.5-2003, Annex G)
+ // Loop on the individual frame[s] and store the information
+ // on the RLE fragments in a RLEFramesInfo.
+ // Note: - when only a single frame is present, this is a
+ // classical image.
+ // - when more than one frame are present, then we are in
+ // the case of a multi-frame image.
+ long frameLength;
+ while ( (frameLength = ReadTagLength(0xfffe, 0xe000)) )
+ {
+ // Parse the RLE Header and store the corresponding RLE Segment
+ // Offset Table information on fragments of this current Frame.
+ // Note that the fragment pixels themselves are not loaded
+ // (but just skipped).
+ long frameOffset = ftell(Fp);
+
+ uint32_t nbRleSegments = ReadInt32();
- //// Reading RLE Segments Offset Table
- uint32_t rleSegmentOffsetTable[15];
- for(int k=1; k<=15; k++)
- {
- ftellRes = ftell(Fp);
- rleSegmentOffsetTable[k] = ReadInt32();
- }
+ uint32_t rleSegmentOffsetTable[15];
+ for( int k = 1; k <= 15; k++ )
+ {
+ rleSegmentOffsetTable[k] = ReadInt32();
+ }
- // skipping (not reading) RLE Segments
- if ( nbRleSegments > 1)
+ // Deduce from both the RLE Header and the frameLength the
+ // fragment length, and again store this info in a
+ // RLEFramesInfo.
+ long rleSegmentLength[15];
+ // skipping (not reading) RLE Segments
+ if ( nbRleSegments > 1)
+ {
+ for(unsigned int k = 1; k <= nbRleSegments-1; k++)
{
- for(unsigned int k = 1; k <= nbRleSegments-1; k++)
- {
- rleSegmentLength[k] = rleSegmentOffsetTable[k+1]
- - rleSegmentOffsetTable[k];
- ftellRes = ftell(Fp);
- SkipBytes(rleSegmentLength[k]);
- }
+ rleSegmentLength[k] = rleSegmentOffsetTable[k+1]
+ - rleSegmentOffsetTable[k];
+ SkipBytes(rleSegmentLength[k]);
}
+ }
- rleSegmentLength[nbRleSegments] = fragmentLength
- - rleSegmentOffsetTable[nbRleSegments];
- ftellRes = ftell(Fp);
- SkipBytes(rleSegmentLength[nbRleSegments]);
- }
+ rleSegmentLength[nbRleSegments] = frameLength
+ - rleSegmentOffsetTable[nbRleSegments];
+ SkipBytes(rleSegmentLength[nbRleSegments]);
- // Make sure that at the end of the item we encounter a 'Sequence
- // Delimiter Item':
- if ( !ReadTag(0xfffe, 0xe0dd) )
- {
- dbg.Verbose(0, "gdcmDocument::Parse7FE0: no sequence delimiter item");
- dbg.Verbose(0, " at end of RLE item sequence");
- }
+ // Store the collected info
+ RLEFrame* newFrameInfo = new RLEFrame;
+ newFrameInfo->NumberFragments = nbRleSegments;
+ for( unsigned int uk = 1; uk <= nbRleSegments; uk++ )
+ {
+ newFrameInfo->Offset[uk] = frameOffset + rleSegmentOffsetTable[uk];
+ newFrameInfo->Length[uk] = rleSegmentLength[uk];
+ }
+ RLEInfo->Frames.push_back( newFrameInfo );
+ }
+
+ // Make sure that at the end of the item we encounter a 'Sequence
+ // Delimiter Item':
+ if ( !ReadTag(0xfffe, 0xe0dd) )
+ {
+ dbg.Verbose(0, "Document::ComputeRLEInfo: no sequence delimiter ");
+ dbg.Verbose(0, " item at end of RLE item sequence");
+ }
+}
+
+/**
+ * \brief Parse pixel data from disk of [multi-]fragment Jpeg encoding.
+ * Compute the jpeg extra information (fragment[s] offset[s] and
+ * length) and store it[them] in \ref JPEGInfo for later pixel
+ * retrieval usage.
+ */
+void Document::ComputeJPEGFragmentInfo()
+{
+ // If you need to, look for comments of ComputeRLEInfo().
+ if ( ! IsJPEGTransferSyntax() )
+ {
+ return;
+ }
+
+ ReadAndSkipEncapsulatedBasicOffsetTable();
+
+ // Loop on the fragments[s] and store the parsed information in a
+ // JPEGInfo.
+ long fragmentLength;
+ while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) )
+ {
+ long fragmentOffset = ftell(Fp);
+
+ // Store the collected info
+ JPEGFragment* newFragment = new JPEGFragment;
+ newFragment->Offset = fragmentOffset;
+ newFragment->Length = fragmentLength;
+ JPEGInfo->Fragments.push_back( newFragment );
+
+ SkipBytes( fragmentLength );
+ }
+
+ // Make sure that at the end of the item we encounter a 'Sequence
+ // Delimiter Item':
+ if ( !ReadTag(0xfffe, 0xe0dd) )
+ {
+ dbg.Verbose(0, "Document::ComputeRLEInfo: no sequence delimiter ");
+ dbg.Verbose(0, " item at end of JPEG item sequence");
}
}
/**
- * \brief Walk recursively the given \ref gdcmDocEntrySet, and feed
+ * \brief Walk recursively the given \ref DocEntrySet, and feed
* the given hash table (\ref TagDocEntryHT) with all the
- * \ref gdcmDocEntry (Dicom entries) encountered.
+ * \ref DocEntry (Dicom entries) encountered.
* This method does the job for \ref BuildFlatHashTable.
- * @param builtHT Where to collect all the \ref gdcmDocEntry encountered
+ * @param builtHT Where to collect all the \ref DocEntry encountered
* when recursively walking the given set.
* @param set The structure to be traversed (recursively).
*/
-void gdcmDocument::BuildFlatHashTableRecurse( TagDocEntryHT& builtHT,
- gdcmDocEntrySet* set )
+void Document::BuildFlatHashTableRecurse( TagDocEntryHT& builtHT,
+ DocEntrySet* set )
{
- if (gdcmElementSet* elementSet = dynamic_cast< gdcmElementSet* > ( set ) )
+ if (ElementSet* elementSet = dynamic_cast< ElementSet* > ( set ) )
{
TagDocEntryHT* currentHT = elementSet->GetTagHT();
for( TagDocEntryHT::const_iterator i = currentHT->begin();
i != currentHT->end();
++i)
{
- gdcmDocEntry* entry = i->second;
- if ( gdcmSeqEntry* seqEntry = dynamic_cast<gdcmSeqEntry*>(entry) )
+ DocEntry* entry = i->second;
+ if ( SeqEntry* seqEntry = dynamic_cast<SeqEntry*>(entry) )
{
ListSQItem& items = seqEntry->GetSQItems();
for( ListSQItem::const_iterator item = items.begin();
return;
}
- if (gdcmSQItem* SQItemSet = dynamic_cast< gdcmSQItem* > ( set ) )
+ if (SQItem* SQItemSet = dynamic_cast< SQItem* > ( set ) )
{
ListDocEntry& currentList = SQItemSet->GetDocEntries();
for (ListDocEntry::iterator i = currentList.begin();
i != currentList.end();
++i)
{
- gdcmDocEntry* entry = *i;
- if ( gdcmSeqEntry* seqEntry = dynamic_cast<gdcmSeqEntry*>(entry) )
+ DocEntry* entry = *i;
+ if ( SeqEntry* seqEntry = dynamic_cast<SeqEntry*>(entry) )
{
ListSQItem& items = seqEntry->GetSQItems();
for( ListSQItem::const_iterator item = items.begin();
/**
* \brief Build a \ref TagDocEntryHT (i.e. a std::map<>) from the current
- * gdcmDocument.
+ * Document.
*
- * The structure used by a gdcmDocument (through \ref gdcmElementSet),
+ * The structure used by a Document (through \ref ElementSet),
* in order to old the parsed entries of a Dicom header, is a recursive
* one. This is due to the fact that the sequences (when present)
* can be nested. Additionaly, the sequence items (represented in
- * gdcm as \ref gdcmSQItem) add an extra complexity to the data
+ * gdcm as \ref SQItem) add an extra complexity to the data
* structure. Hence, a gdcm user whishing to visit all the entries of
* a Dicom header will need to dig in the gdcm internals (which
* implies exposing all the internal data structures to the API).
* Dicom entries in a flat structure (a \ref TagDocEntryHT i.e. a
* std::map<>).
* \warning Of course there is NO integrity constrain between the
- * returned \ref TagDocEntryHT and the \ref gdcmElementSet used
- * to build it. Hence if the underlying \ref gdcmElementSet is
+ * returned \ref TagDocEntryHT and the \ref ElementSet used
+ * to build it. Hence if the underlying \ref ElementSet is
* altered, then it is the caller responsability to invoke
* \ref BuildFlatHashTable again...
* @return The flat std::map<> we juste build.
*/
-TagDocEntryHT* gdcmDocument::BuildFlatHashTable()
+TagDocEntryHT* Document::BuildFlatHashTable()
{
TagDocEntryHT* FlatHT = new TagDocEntryHT;
BuildFlatHashTableRecurse( *FlatHT, this );
/**
- * \brief Compares two documents, according to \ref gdcmDicomDir rules
+ * \brief Compares two documents, according to \ref DicomDir rules
* \warning Does NOT work with ACR-NEMA files
* \todo Find a trick to solve the pb (use RET fields ?)
* @param document
* @return true if 'smaller'
*/
-bool gdcmDocument::operator<(gdcmDocument &document)
+bool Document::operator<(Document &document)
{
// Patient Name
std::string s1 = GetEntryByNumber(0x0010,0x0010);
return false;
}
+} // end namespace gdcm
//-----------------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff